Understanding how robust the molecular clock is a critical step for many evolutionary analyses. Usually when I get given a set of aligned sequences I turn to TempEst to test the ‘clocklikeness’ of the data. However, after the release of ‘TIPDATINGBEAST’ (I’ll call it TDBEAST fr short) I may turn to TempEst much less often. Whist TempEst is useful in getting some qualitative idea of the temporal signal in the data but I find it annoying that its hard to drill down to find what sequences sequences that are leading to bias. Furthermore, TempEst is sensitive to the input tree which can lead to problems and I have had issues with guessDates as well which is slightly irritating. TDBEAST solves lots of these issues and more and provides a robust method to test how ‘clock-like’ your sequences are. The TDBEAST R package does 2 things using BEAST log files and .xml files:
1. Uses a date randomization test to measure temporal signal and provides a nice visualization to check results.
2. Uses a leave one out cross validation to work out the likely culprits that could be skewing results. These sequences, for example, could have the wrong date assigned to them by mistake – this is a real problem when working on sequences from the field.
Whilst I’m having a few teething issues with the code, overall the ‘how to’ guide is excellent and the code seems straight forward. TDBEAST definitely seems like a valuable addition to my phylogenetic tool box.
Here are the links: http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12603/full